GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Croceitalea dokdonensis DOKDO 023

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_054559826.1 I595_RS12740 ABC transporter ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>NCBI__GCF_001306415.1:WP_054559826.1
          Length = 325

 Score =  110 bits (275), Expect = 3e-29
 Identities = 69/228 (30%), Positives = 123/228 (53%), Gaps = 5/228 (2%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           ML+ D +S  Y     L DVS  ++KG  ++++G +G+GKSTLL  + G  +   G++ +
Sbjct: 1   MLAVDSISFSYANKPILKDVSFSIEKGTHLSIMGESGSGKSTLLKAIYGLLELEKGTVFW 60

Query: 61  EGEELVGLPSSTIM--RKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLE 118
             E+++G P+  ++   K +  V +   +    TV EN+A      + D +Q ++ ++L 
Sbjct: 61  GKEQVLG-PNYNLVPGEKYMKYVAQDFDLMPFTTVTENIAEHLSAFEMDSHQARITELLH 119

Query: 119 LFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQI-FEIIE 177
           +   ++E    +   +SGG+QQ +A+ RAL  +P++LLLDEP   +      ++ +++  
Sbjct: 120 II-EMEEFAHVKVKNLSGGQQQRVALARALAQEPEVLLLDEPFSSIDQFKKNELRYKLFP 178

Query: 178 QLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPK 225
            LR +G+TV     + N  L  AD   VL+NG I+ H+    L   PK
Sbjct: 179 YLREKGITVINASHDPNDVLAFADETIVLKNGEILAHEPTVQLYQIPK 226


Lambda     K      H
   0.318    0.136    0.374 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 138
Number of extensions: 8
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 233
Length of database: 325
Length adjustment: 25
Effective length of query: 208
Effective length of database: 300
Effective search space:    62400
Effective search space used:    62400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory